I've been using Mystique with the 2 column/right sidebar settings, with no problems, for several months. Today I upgraded to WP 3.0, and things were still fine after that, so I don't think this is necessarily a 3.0 issue. Anyway, shortly thereafter, when on the dashboard I saw that an upgrade to Mystique 2.3.1 was available, I upgraded to that. Now, I did not download it, save it on my pc, upload with ftp, etc.; WP just did it, and said that I had been upgraded successfully -- and that shows as the theme I'm using.
After the upgrade, I noticed that my right sidebar was wider than before, presumably having returned to the default setting. I should mention that I like to post lots of photos, so previously I had reduced the sidebar enough to fit photos at 768 pixels. However, when I went to the "Mystique settings" page, when I tried to change the column size to fit those larger photos, I couldn't do it without the sidebar disappearing. And I guess this probably explains why: there's a box of text above the sidebar, saying "You activated the 2nd sidebar. Add widgets here from the Dashboard to remove this message." This bizarre message is not visible on the public view of my blog, just when looking at it at the Mystique settings page. Now, I do have lots of widgets in my sidebar, and I had one in my footer as well. When I first brought up the settings page, I noticed that that footer widget was now at the top, in what appeared to be a third column/2nd sidebar. I deleted that widget, to see if that would correct things, but it hasn't. I'm guessing this all has to do with a new feature I see on Mystique 2.3.1 -- at the bottom where there's numbers for all the previous pages, which is a GREAT feature and a vast improvement over having to hit "Older entries" over and over.
However, as great as that new feature is, for my site it's really urgent to have this resolved ASAP, as I've already posted a lot of photos that now have good portions of them cut off.
Sorry for going on at such length, but this is not easy one to describe.
Thanks!